In Never trust a hypothesis?, Suicyte pens a good write up of the current state of big biology and small biology_
Imagine an old fashioned biologist, throwing out his hypothesis-driven fishing line into the pond of science, hoping that a particular fish will be attracted by the highly specific bait. Then imagine a group of contemporary way cool high-throughput researchers (those guys always come in large groups), trawling the same pond with their fishing net, catching literally thousands of fishes in the same time.
He goes on to talk about ways to think about the reliability of information gained in both types of studies. It's a good read, but I have just one one minor complaint, which I commented on and will repost here_
Good write-up of the current situation in biology.
My only complaint is that I think your fisherman analogy sets big science and little science up as adversarial, where I see it as more of a synergistic relationship.
Big biology (high-throughput screens, genome-wide association studies, etc) is there to narrow down the list of potential targets to a manageable size. This knowledge allows your lone fisherman to test 2 or 3 likely hypotheses, rather than facing overwheming numbers of gene or proteins in a list.
I understand that the two approaches are competing for grant dollars right now, but I don't think it's a situation that will last much longer. Sequencing genomes is getting ridiculously cheap, and I expect that we'll see similar advances in high-throughput proteomics over the next 20 years of so.
As the high-throughput technologies mature, they'll require less R&D funding, and the small science labs will be able to pick up that money and go back to what they do best - proving hypotheses. The difference is, at that point, they'll be doing it with vastly more information at their disposal. I see it as a win-win situation.